id: Q99424
gene_symbol: ACOX2
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ACOX2 is the human peroxisomal branched-chain acyl-CoA oxidase (EC 1.3.3.6), a
  FAD-dependent flavoenzyme of the acyl-CoA oxidase family. It catalyzes the first,
  oxygen-dependent and rate-limiting dehydrogenation step of peroxisomal beta-oxidation,
  removing two hydrogens and introducing a trans-2,3 double bond into the acyl-CoA
  substrate while generating hydrogen peroxide as a byproduct. Its principal physiological
  substrates are the C27 bile-acid intermediates (25S)-3alpha,7alpha,12alpha-trihydroxy-
  cholestanoyl-CoA (THCA-CoA) and dihydroxycholestanoyl-CoA (DHCA-CoA); ACOX2 initiates the
  side-chain shortening that converts these C27 cholestanoic acids into the mature C24 bile
  acids (cholic and chenodeoxycholic acid). It also oxidizes 2-methyl-branched-chain fatty
  acyl-CoA esters such as (2S)-pristanoyl-CoA (with redundancy to ACOX3) and monomethyl
  branched-chain fatty acids, acting stereospecifically on (2S)-methyl isomers, and can
  oxidize straight-chain acyl-CoAs with low efficiency. ACOX2 is a homodimer that resides in
  the peroxisomal matrix, imported via its C-terminal SKL (PTS1) targeting signal. It is
  expressed in many tissues, most abundantly in liver, kidney and heart. Loss-of-function
  causes ACOX2 deficiency (congenital bile acid synthesis defect 6, CBAS6), an autosomal
  recessive disorder marked by accumulation of toxic C27 bile-acid intermediates, persistent
  hypertransaminasemia and liver fibrosis, with variable neurological features.
existing_annotations:
- term:
    id: GO:0005504
    label: fatty acid binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Fatty acid binding propagated by phylogenetic inference. Substrate binding is implicit
      in the acyl-CoA oxidase catalytic mechanism, but a bare "fatty acid binding" molecular
      function term is uninformative for this enzyme, whose informative MF is its acyl-CoA
      oxidase (dehydrogenase) activity. Retained but flagged as an over-annotation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      ACOX2 acts on acyl-CoA thioesters (branched-chain and C27 bile-acid CoA esters), not
      on free fatty acids, and its informative molecular function is captured by the acyl-CoA
      oxidase activity terms. A generic "fatty acid binding" adds little functional
      information and is more precisely represented by the catalytic MF terms.
    propagation_review:
      root_cause: TERM_SCOPING_PROBLEM
      failure_modes:
      - GRANULARITY_MISMATCH
      - ROLE_CONFLATION
      source_entities:
      - source_id: PANTHER:PTN000097533
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          Family-level "fatty acid binding" propagated from the acyl-CoA oxidase clade; ACOX2
          acts on acyl-CoA thioesters, and the informative MF is its acyl-CoA oxidase activity.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: >-
        Involved in peroxisomal beta-oxidation of branched-chain
        fatty acids (BCFAs) and bile acids intermediates.
- term:
    id: GO:0033540
    label: fatty acid beta-oxidation using acyl-CoA oxidase
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetically inferred involvement in fatty acid beta-oxidation via an acyl-CoA
      oxidase. This is exactly the pathway ACOX2 participates in, catalyzing the first
      oxidase step of peroxisomal beta-oxidation of branched-chain and bile-acid CoA esters.
    action: ACCEPT
    reason: >-
      Directly supported by experimental data (IDA/IMP from PMID:27884763) and by the UniProt
      PATHWAY assignment to peroxisomal fatty acid beta-oxidation. The IBA is at an
      appropriate level of specificity for an acyl-CoA-oxidase family enzyme.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Lipid metabolism; peroxisomal fatty acid beta-oxidation.'
- term:
    id: GO:0120524
    label: long-chain fatty acyl-CoA oxidase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Long-chain acyl-CoA oxidase activity inferred phylogenetically. ACOX2 can oxidize
      straight-chain long-chain acyl-CoAs (e.g. hexadecanoyl-CoA/C16-CoA) but only with low
      efficiency; its physiological substrates are branched-chain and C27 bile-acid CoA
      esters. Retained but noted as a minor/low-efficiency activity rather than a core function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      UniProt explicitly states ACOX2 oxidizes straight-chain acyl-CoAs (C10-CoA, C16-CoA)
      only with low efficiency; long-chain straight-chain oxidation is the physiological role
      of ACOX1, not ACOX2. The term is not wrong (there is measurable C16-CoA activity) but
      over-states its importance relative to the branched-chain/bile-acid core function.
    propagation_review:
      root_cause: TERM_SCOPING_PROBLEM
      failure_modes:
      - FUNCTIONAL_DIVERGENCE
      - GRANULARITY_MISMATCH
      source_entities:
      - source_id: UniProtKB:Q15067
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          Long-chain acyl-CoA oxidase activity fits ACOX1-type members; ACOX2 oxidizes
          straight long-chain acyl-CoAs only with low efficiency, its physiological substrates
          being branched-chain and C27 bile-acid CoA esters.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'acyl CoAs such as C10-CoA and C16-CoA with low efficiency'
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetically inferred peroxisomal localization/activity. ACOX2 carries a C-terminal
      SKL (PTS1) signal and is directly demonstrated to be peroxisomal in human liver, and is
      active within the peroxisome.
    action: ACCEPT
    reason: >-
      Consistent with strong experimental evidence (IDA in PMID:8943006 and PMID:2079609; IMP
      in PMID:27884763) and the UniProt SUBCELLULAR LOCATION. is_active_in is appropriate for
      a matrix enzyme acting inside the peroxisome.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Peroxisome'
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      FAD binding inferred phylogenetically. ACOX2 is a FAD-dependent flavoprotein oxidase;
      FAD is an essential cofactor for the oxidative dehydrogenation reaction.
    action: ACCEPT
    reason: >-
      Supported by the UniProt COFACTOR annotation (FAD) and by the flavoprotein character of
      the whole acyl-CoA oxidase family. Reactome also describes the ACOX2:FAD holoenzyme.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Name=FAD; Xref=ChEBI:CHEBI:57692'
- term:
    id: GO:0000038
    label: very long-chain fatty acid metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Involvement in very long-chain fatty acid metabolism inferred phylogenetically. ACOX2's
      physiological substrates are 2-methyl-branched-chain acyl-CoAs and C27 bile-acid
      intermediates, not straight very-long-chain fatty acids, which are the substrates of
      ACOX1. This appears to be over-propagation across the acyl-CoA oxidase clade.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Straight VLCFA beta-oxidation is the role of ACOX1 (palmitoyl-CoA oxidase). Human liver
      enzymology (PMID:2079609) distinguishes the separate trihydroxycoprostanoyl-CoA oxidase
      (ACOX2) from the palmitoyl-CoA oxidase, and UniProt notes only low-efficiency
      straight-chain activity for ACOX2. The VLCFA-metabolism assignment likely reflects
      family-level IBA transfer rather than ACOX2's actual physiological substrate range.
    propagation_review:
      root_cause: PROPAGATION_BAD
      failure_modes:
      - FUNCTIONAL_DIVERGENCE
      source_entities:
      - source_id: UniProtKB:Q15067
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          Very-long-chain fatty acid metabolism is the role of ACOX1-type members; human liver
          enzymology (PMID:2079609) separates the trihydroxycoprostanoyl-CoA oxidase (ACOX2)
          from the palmitoyl-CoA oxidase, so this process should not transfer to ACOX2.
    supported_by:
    - reference_id: PMID:2079609
      supporting_text: >-
        The results show that human liver, as rat liver, contains a separate
        trihydroxycoprostanoyl-CoA oxidase.
- term:
    id: GO:0033791
    label: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase
      activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      THCA-CoA oxidase (24-hydroxylase) activity inferred phylogenetically, with ACOX2 itself
      among the supporting genes (UniProtKB:Q99424 in the WITH/FROM). This is the
      bile-acid-specific reaction ACOX2 catalyzes on the C27 intermediate THCA-CoA.
    action: ACCEPT
    reason: >-
      Directly supported by experimental evidence (IDA in PMID:27884763) and by the UniProt
      catalytic activity for (25S)-THCA-CoA oxidation (Rhea:46728). This is a core molecular
      function.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: >-
        Reaction=(25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-
- term:
    id: GO:0003997
    label: acyl-CoA oxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Acyl-CoA oxidase activity (EC 1.3.3.6) assigned electronically from InterPro/Rhea. This
      is the defining molecular function of ACOX2 and is experimentally confirmed.
    action: ACCEPT
    reason: >-
      This parent MF term precisely captures ACOX2's biochemistry (a 2,3-saturated acyl-CoA +
      O2 -> a (2E)-enoyl-CoA + H2O2, EC 1.3.3.6), confirmed experimentally in PMID:27884763
      and via the UniProt catalytic activity (Rhea:38959). It is the best single molecular
      function term for this enzyme.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Reaction=a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2;'
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal localization assigned electronically (InterPro / UniProt SubCell). Confirmed
      by direct experimental evidence.
    action: ACCEPT
    reason: >-
      Consistent with the UniProt SUBCELLULAR LOCATION (Peroxisome) and multiple experimental
      annotations (IDA/IMP). The SKL C-terminal PTS1 targets the protein to the peroxisome.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Peroxisome'
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal matrix localization assigned by ARBA machine-learning model. As a soluble
      PTS1-targeted matrix enzyme, ACOX2 resides in the peroxisomal matrix, consistent with
      Reactome placing its reactions in the peroxisomal matrix.
    action: ACCEPT
    reason: >-
      ACOX2 is a soluble matrix flavoenzyme (SKL/PTS1 import, not membrane-bound). This is a
      more specific and accurate compartment than the parent "peroxisome" term, and matches
      the Reactome curated location of its catalytic reactions.
    supported_by:
    - reference_id: Reactome:R-HSA-192335
      supporting_text: This dehydrogenation reaction occurs in the peroxisomal matrix.
- term:
    id: GO:0006631
    label: fatty acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      Broad fatty acid metabolic process assigned from InterPro. Correct but general; ACOX2's
      specific role is captured by fatty acid beta-oxidation and bile acid biosynthetic
      process terms.
    action: ACCEPT
    reason: >-
      A true but broad parent process term. ACOX2 participates in fatty acid metabolism
      (peroxisomal beta-oxidation of branched-chain fatty acids). Kept as an accurate
      high-level annotation; more specific BP terms are also present.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: >-
        Involved in peroxisomal beta-oxidation of branched-chain
        fatty acids (BCFAs) and bile acids intermediates.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      Fatty acid beta-oxidation assigned electronically from InterPro. ACOX2 catalyzes the
      first oxidase step of peroxisomal beta-oxidation, so this is an accurate parent of the
      more specific "fatty acid beta-oxidation using acyl-CoA oxidase" term.
    action: ACCEPT
    reason: >-
      Directly supported by the UniProt PATHWAY (peroxisomal fatty acid beta-oxidation) and
      by experimental data. This is a core biological process for ACOX2.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Lipid metabolism; peroxisomal fatty acid beta-oxidation.'
- term:
    id: GO:0016402
    label: pristanoyl-CoA oxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      Pristanoyl-CoA oxidase activity assigned from Rhea (RHEA:40459). ACOX2 oxidizes
      (2S)-pristanoyl-CoA, a 2-methyl-branched-chain fatty acyl-CoA, though it acts
      redundantly with ACOX3 for this substrate.
    action: ACCEPT
    reason: >-
      Supported by the UniProt catalytic activity for (2S)-pristanoyl-CoA (Rhea:40459,
      ECO:0000269|PubMed:29287774). This is a genuine branched-chain fatty acyl-CoA oxidase
      activity of ACOX2.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Reaction=(2S)-pristanoyl-CoA + O2 = (2E)-pristenoyl-CoA + H2O2;'
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: enables
  review:
    summary: >-
      Root-level oxidoreductase activity from ARBA. Correct but very general; ACOX2's
      oxidoreductase function is precisely captured by acyl-CoA oxidase activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is a high-level grouping term that is technically true (ACOX2 is an oxidoreductase)
      but uninformative given the specific acyl-CoA oxidase activity (EC 1.3.3.6) is already
      annotated. Retained but flagged as too general.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: EC=1.3.3.6
- term:
    id: GO:0016627
    label: oxidoreductase activity, acting on the CH-CH group of donors
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Oxidoreductase acting on the CH-CH group of donors, from InterPro. This is the correct
      mechanistic class (introduction of a C2-C3 double bond), an intermediate parent of
      acyl-CoA oxidase activity.
    action: ACCEPT
    reason: >-
      Accurate mechanistic parent term: ACOX2 desaturates the alpha-beta (CH-CH) bond of the
      acyl-CoA. It is subsumed by the more specific acyl-CoA oxidase activity but is not
      incorrect. Kept as an accurate intermediate-level annotation.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: >-
        introduces a trans double bond between the alpha and beta
        carbons of the acyl CoA molecules
- term:
    id: GO:0033540
    label: fatty acid beta-oxidation using acyl-CoA oxidase
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Fatty acid beta-oxidation using acyl-CoA oxidase, assigned by ARBA. This is the precise
      pathway term for ACOX2 and is also supported experimentally.
    action: ACCEPT
    reason: >-
      Duplicate of the experimentally supported (IDA/IMP, PMID:27884763) and IBA annotations
      for the same term. Precisely describes ACOX2's contribution to peroxisomal
      beta-oxidation.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Lipid metabolism; peroxisomal fatty acid beta-oxidation.'
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      FAD binding assigned from InterPro. Duplicate of the IBA/ISS FAD-binding annotations;
      ACOX2 is a FAD-dependent flavoprotein.
    action: ACCEPT
    reason: >-
      Supported by the UniProt COFACTOR (FAD) annotation. FAD is the essential redox cofactor
      of this oxidase.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Name=FAD; Xref=ChEBI:CHEBI:57692'
- term:
    id: GO:0071949
    label: FAD binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      FAD binding (GO:0071949) assigned from InterPro. Semantically equivalent to the
      GO:0050660 FAD-binding annotations; both describe binding of the FAD cofactor.
    action: ACCEPT
    reason: >-
      Supported by the UniProt COFACTOR (FAD) annotation. Retained; this is a valid (if
      redundant with GO:0050660) representation of FAD cofactor binding.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Name=FAD; Xref=ChEBI:CHEBI:57692'
- term:
    id: GO:0120523
    label: medium-chain fatty acyl-CoA oxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      Medium-chain acyl-CoA oxidase activity from Rhea (RHEA:40179, decanoyl-CoA). ACOX2 can
      oxidize the medium-chain substrate decanoyl-CoA (C10-CoA), but UniProt characterizes
      straight-chain oxidation as low efficiency.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      There is measurable in vitro activity on decanoyl-CoA (Rhea:40179, PubMed:29287774), so
      the term is not wrong, but UniProt explicitly notes straight-chain acyl-CoA oxidation
      (C10-CoA, C16-CoA) is low efficiency. This is a minor activity, not a core physiological
      function, which is branched-chain and bile-acid CoA-ester oxidation.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'acyl CoAs such as C10-CoA and C16-CoA with low efficiency'
- term:
    id: GO:0120524
    label: long-chain fatty acyl-CoA oxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      Long-chain acyl-CoA oxidase activity from Rhea (RHEA:40167, hexadecanoyl-CoA). Duplicate
      of the IBA long-chain annotation; represents low-efficiency straight-chain activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      In vitro C16-CoA (hexadecanoyl-CoA) oxidation exists (Rhea:40167), but UniProt states it
      is low efficiency; straight-chain long-chain oxidation is the physiological role of
      ACOX1. Flagged as over-annotation relative to ACOX2's branched-chain/bile-acid core.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'acyl CoAs such as C10-CoA and C16-CoA with low efficiency'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a high-throughput affinity-capture interactome screen
      (BioPlex; ACOX2 with STRN3, UniProtKB:Q13033). Uninformative molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Per curation guidelines, bare "protein binding" (GO:0005515) is uninformative. This
      interaction derives from a genome-scale interactome mapping study, not a functional
      characterization; there is no evidence it reflects a physiologically meaningful complex
      of ACOX2. Retained (not removed, per policy for experimental IPIs) but marked as
      over-annotated.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Q99424; Q13033: STRN3'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from the HuRI binary interactome map (ACOX2 with DYNLT1,
      UniProtKB:P63172). Uninformative molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare "protein binding" from a systematic binary (Y2H) interactome screen is
      uninformative and does not point to a specific biochemical function of ACOX2. Retained
      per policy for experimental IPIs but flagged as over-annotated.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Q99424; P63172: DYNLT1'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a proteome-scale interactome network study (BioPlex 3.0;
      ACOX2 with STRN3, UniProtKB:Q13033). Uninformative molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare "protein binding" from a high-throughput interactome dataset is uninformative for
      curation and does not establish a functionally relevant ACOX2 complex. Retained per
      policy for experimental IPIs but flagged as over-annotated.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Q99424; Q13033: STRN3'
- term:
    id: GO:0006699
    label: bile acid biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:27884763
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental evidence that ACOX2 is involved in bile acid biosynthesis: patients
      with the R225W mutation accumulate C27 intermediates and lack C24 bile acids, and
      overexpression of wild-type (but not mutant) ACOX2 enhances biotransformation of THCA
      into cholic acid. This is a core biological process.
    action: ACCEPT
    reason: >-
      Strong IDA evidence from PMID:27884763 places ACOX2 in the peroxisomal side-chain
      shortening of C27 cholestanoic acids to C24 bile acids. This is one of ACOX2's two core
      physiological roles.
    supported_by:
    - reference_id: PMID:27884763
      supporting_text: >-
        Acyl-CoA oxidase (ACOX2) is involved in the shortening of C27
        cholesterol derivatives to generate C24 bile acids.
    - reference_id: PMID:27884763
      supporting_text: >-
        THCA biotransformation into cholic acid was enhanced in cells overexpressing
        ACOX2, but not in those overexpressing mutACOX2.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9033235
  qualifier: located_in
  review:
    summary: >-
      Cytosol localization from a Reactome peroxisomal-import reaction (PEX5 cargo
      translocating from cytosol to the peroxisomal matrix). This reflects the transient
      cytosolic import intermediate of matrix proteins, not the compartment where ACOX2 is
      catalytically active.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      ACOX2 is a PTS1 (SKL) matrix enzyme; peroxisomal matrix proteins are synthesized in the
      cytosol and imported post-translationally, so a transient cytosolic pool exists, but the
      functional/steady-state location is the peroxisomal matrix. The cytosol annotation
      captures the import-pathway transit state rather than the site of ACOX2 activity.
    supported_by:
    - reference_id: Reactome:R-HSA-9033235
      supporting_text: Cargo of PEX5S,L translocates from the cytosol to the peroxisomal matrix
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9033236
  qualifier: located_in
  review:
    summary: >-
      Cytosol localization from a Reactome peroxisomal-import docking reaction (PEX5:cargo
      binding the PEX13/PEX14 docking-translocation module). Like the sibling annotation, this
      reflects the cytosolic import intermediate, not ACOX2's catalytic compartment.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Same rationale as the other cytosol annotation: this is the transient cytosolic
      import/docking state of the PTS1-targeted matrix enzyme, not its functional location,
      which is the peroxisomal matrix.
    supported_by:
    - reference_id: Reactome:R-HSA-9033236
      supporting_text: >-
        PEX5S,L:Cargo binds PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IMP
  original_reference_id: PMID:27884763
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal localization confirmed by immunofluorescence in HepG2 cells overexpressing
      wild-type and R225W-mutant ACOX2; both showed peroxisomal localization. Direct
      experimental support for the peroxisome location.
    action: ACCEPT
    reason: >-
      PMID:27884763 experimentally demonstrates peroxisomal localization of ACOX2 (both WT and
      mutant). Consistent with the UniProt SUBCELLULAR LOCATION and the IDA localizations.
    supported_by:
    - reference_id: PMID:27884763
      supporting_text: >-
        Immunofluorescence studies showed similar
        protein size and peroxisomal localization for both normal and mutated variants.
- term:
    id: GO:0033540
    label: fatty acid beta-oxidation using acyl-CoA oxidase
  evidence_type: IDA
  original_reference_id: PMID:27884763
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental evidence for ACOX2's role in acyl-CoA-oxidase-mediated
      beta-oxidation, shown via its bile-acid intermediate (THCA) processing that requires
      functional ACOX2. Core biological process.
    action: ACCEPT
    reason: >-
      PMID:27884763 demonstrates that functional ACOX2 is required for the oxidase step that
      processes C27 bile-acid CoA intermediates during peroxisomal beta-oxidation. Precise
      pathway term.
    supported_by:
    - reference_id: PMID:27884763
      supporting_text: >-
        THCA biotransformation into cholic acid was enhanced in cells overexpressing
        ACOX2, but not in those overexpressing mutACOX2.
- term:
    id: GO:0033791
    label: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase
      activity
  evidence_type: IDA
  original_reference_id: PMID:27884763
  qualifier: enables
  review:
    summary: >-
      Direct experimental evidence for THCA-CoA oxidase activity: wild-type ACOX2, but not the
      R225W mutant, enhances biotransformation of THCA to cholic acid, establishing this
      specific catalytic activity on the C27 bile-acid intermediate. Core molecular function.
    action: ACCEPT
    reason: >-
      IDA evidence in PMID:27884763 directly supports ACOX2's activity on the C27
      trihydroxycholestanoyl-CoA substrate. Corresponds to the UniProt catalytic activity
      (Rhea:46728) for (25S)-THCA-CoA oxidation. This is a core molecular function.
    supported_by:
    - reference_id: PMID:27884763
      supporting_text: >-
        THCA biotransformation into cholic acid was enhanced in cells overexpressing
        ACOX2, but not in those overexpressing mutACOX2.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal localization transferred by sequence similarity from ACOX1 (UniProtKB:P07872).
      Consistent with the direct experimental peroxisomal localization of ACOX2.
    action: ACCEPT
    reason: >-
      Redundant with strong direct evidence (IDA/IMP) for peroxisomal localization. The SKL
      PTS1 signal and experimental data confirm the peroxisome location.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Peroxisome'
- term:
    id: GO:0033540
    label: fatty acid beta-oxidation using acyl-CoA oxidase
  evidence_type: IMP
  original_reference_id: PMID:27884763
  qualifier: involved_in
  review:
    summary: >-
      Involvement in acyl-CoA-oxidase-mediated beta-oxidation supported by mutational
      phenotype: the R225W mutation reduces ACOX2 function, and patients accumulate C27
      bile-acid intermediates with loss of C24 bile acids. Core biological process.
    action: ACCEPT
    reason: >-
      IMP evidence (loss-of-function R225W phenotype) in PMID:27884763 confirms ACOX2's
      requirement for the peroxisomal acyl-CoA-oxidase beta-oxidation of C27 intermediates.
    supported_by:
    - reference_id: PMID:27884763
      supporting_text: >-
        The patient's serum and urine showed negligible amounts of C24 bile
        acids, but augmented levels of C27 intermediates
- term:
    id: GO:0033791
    label: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase
      activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      THCA-CoA oxidase activity transferred by sequence similarity from the rat ortholog
      (UniProtKB:O02767, THCC oxidase). Consistent with the direct experimental activity for
      human ACOX2.
    action: ACCEPT
    reason: >-
      Redundant with the IDA/IBA annotations for the same activity. ACOX2 is the human homolog
      of rat trihydroxycoprostanoyl-CoA oxidase, and the ISS transfer from the rat ortholog is
      well-founded.
    supported_by:
    - reference_id: PMID:8943006
      supporting_text: >-
        the hBRCACox is the human homolog of rat trihydroxycoprostanoyl-CoA
        oxidase (rTHCCox)
- term:
    id: GO:0042803
    label: protein homodimerization activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      Homodimerization activity transferred by sequence similarity from ACOX1 (UniProtKB:P07872).
      UniProt annotates ACOX2 as a homodimer (by similarity).
    action: ACCEPT
    reason: >-
      Supported by the UniProt SUBUNIT annotation (Homodimer, by similarity). Acyl-CoA oxidase
      family members characteristically form homodimers. Retained as a by-similarity
      structural/quaternary annotation.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'SUBUNIT: Homodimer.'
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      FAD binding transferred by sequence similarity from ACOX1 (UniProtKB:P07872). ACOX2 is a
      FAD flavoprotein. Redundant with the IBA/IEA FAD-binding annotations.
    action: ACCEPT
    reason: >-
      Supported by the UniProt COFACTOR (FAD) annotation and the flavoprotein nature of the
      acyl-CoA oxidase family. FAD is the essential redox cofactor.
    supported_by:
    - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
      supporting_text: 'Name=FAD; Xref=ChEBI:CHEBI:57692'
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-192335
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal matrix localization from Reactome, tied to the curated reaction in which
      ACOX2 dehydrogenates 25(S) THCA-CoA in the peroxisomal matrix. Accurate compartment for
      this soluble matrix enzyme.
    action: ACCEPT
    reason: >-
      Reactome explicitly places the ACOX2-catalyzed THCA-CoA dehydrogenation in the
      peroxisomal matrix. This is the accurate, specific compartment for the soluble
      PTS1-targeted enzyme.
    supported_by:
    - reference_id: Reactome:R-HSA-192335
      supporting_text: This dehydrogenation reaction occurs in the peroxisomal matrix.
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-193369
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal matrix localization from Reactome, tied to the curated reaction in which
      ACOX2 dehydrogenates 25(S) DHCA-CoA. Accurate compartment for this soluble matrix enzyme.
    action: ACCEPT
    reason: >-
      Reactome places the ACOX2-catalyzed DHCA-CoA dehydrogenation in the peroxisomal matrix,
      consistent with the enzyme's soluble matrix localization. Accurate, specific compartment.
    supported_by:
    - reference_id: Reactome:R-HSA-193369
      supporting_text: 25(S) DHCA-CoA is dehydrogenated to 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-389889
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal matrix localization from Reactome, tied to the curated reaction in which
      ACOX2:FAD oxidizes (2S)-pristanoyl-CoA. Accurate compartment for this soluble matrix
      enzyme.
    action: ACCEPT
    reason: >-
      Reactome places the ACOX2-catalyzed pristanoyl-CoA oxidation in the peroxisomal matrix,
      consistent with the enzyme's soluble matrix localization. Accurate, specific compartment.
    supported_by:
    - reference_id: Reactome:R-HSA-389889
      supporting_text: >-
        monomeric peroxisomal ACOX2 (bound to FAD
        cofactor) catalyzes the reaction of (2S)-pristanoyl-CoA
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9033235
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal matrix localization from Reactome, from the peroxisomal-import reaction in
      which PEX5 cargo (including ACOX2) is translocated into the matrix. Accurate destination
      compartment.
    action: ACCEPT
    reason: >-
      The reaction describes cargo translocation into the peroxisomal matrix, which is ACOX2's
      functional destination. Consistent with the other matrix annotations and experimental
      data.
    supported_by:
    - reference_id: Reactome:R-HSA-9033235
      supporting_text: Cargo of PEX5S,L translocates from the cytosol to the peroxisomal matrix
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:8943006
  qualifier: located_in
  review:
    summary: >-
      Direct experimental peroxisomal localization: the human branched-chain acyl-CoA oxidase
      carries a C-terminal SKL PTS1 signal and was shown to be peroxisomal (and absent from
      Zellweger livers by immunoblot/immunocytochemistry). Core localization.
    action: ACCEPT
    reason: >-
      PMID:8943006 provides direct evidence for peroxisomal localization (SKL PTS1; absence in
      Zellweger patients, a peroxisome biogenesis disorder). Strong support for the peroxisome
      location.
    supported_by:
    - reference_id: PMID:8943006
      supporting_text: >-
        The C-terminal tripeptide of the protein is SKL, a
        known peroxisome targeting signal.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:2079609
  qualifier: located_in
  review:
    summary: >-
      Peroxisomal localization inferred from human liver enzymology establishing a separate
      peroxisomal trihydroxycoprostanoyl-CoA oxidase (ACOX2), distinct from palmitoyl-CoA
      oxidase, catalyzing the first step of peroxisomal beta-oxidation.
    action: ACCEPT
    reason: >-
      PMID:2079609 demonstrates a distinct peroxisomal trihydroxycoprostanoyl-CoA oxidase in
      human liver (i.e. ACOX2), supporting its peroxisomal localization. Consistent with all
      other localization evidence.
    supported_by:
    - reference_id: PMID:2079609
      supporting_text: >-
        Fatty acyl-CoAs as well as the CoA esters of the bile acid intermediates di- and
        trihydroxycoprostanic acids are beta-oxidized in peroxisomes.
core_functions:
- description: >-
    Peroxisomal branched-chain acyl-CoA oxidase (EC 1.3.3.6): FAD-dependent oxidase that
    catalyzes the first, O2-dependent dehydrogenation step of peroxisomal beta-oxidation,
    introducing a trans-2,3 double bond into the acyl-CoA and producing H2O2.
  molecular_function:
    id: GO:0003997
    label: acyl-CoA oxidase activity
  directly_involved_in:
  - id: GO:0006635
    label: fatty acid beta-oxidation
  supported_by:
  - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
    supporting_text: 'Reaction=a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2;'
  locations:
  - id: GO:0005782
    label: peroxisomal matrix
- description: >-
    Initiates side-chain shortening of C27 bile-acid intermediates by oxidizing
    (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA (THCA-CoA) and DHCA-CoA,
    contributing to peroxisomal synthesis of the mature C24 bile acids; loss of this activity
    causes ACOX2 deficiency (CBAS6) with C27 intermediate accumulation.
  molecular_function:
    id: GO:0033791
    label: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity
  directly_involved_in:
  - id: GO:0006699
    label: bile acid biosynthetic process
  supported_by:
  - reference_id: PMID:27884763
    supporting_text: >-
      Acyl-CoA oxidase (ACOX2) is involved in the shortening of C27
      cholesterol derivatives to generate C24 bile acids.
  locations:
  - id: GO:0005782
    label: peroxisomal matrix
- description: >-
    Oxidizes 2-methyl-branched-chain fatty acyl-CoA esters such as (2S)-pristanoyl-CoA
    (stereospecific for (2S)-methyl isomers), functioning in peroxisomal beta-oxidation of
    branched-chain fatty acids with redundancy to ACOX3.
  molecular_function:
    id: GO:0016402
    label: pristanoyl-CoA oxidase activity
  directly_involved_in:
  - id: GO:0006635
    label: fatty acid beta-oxidation
  supported_by:
  - reference_id: file:human/ACOX2/ACOX2-uniprot.txt
    supporting_text: 'Reaction=(2S)-pristanoyl-CoA + O2 = (2E)-pristenoyl-CoA + H2O2;'
  locations:
  - id: GO:0005782
    label: peroxisomal matrix
proposed_new_terms: []
suggested_questions:
- question: >-
    What is the relative in vivo contribution of ACOX2 vs ACOX3 to pristanoyl-CoA /
    branched-chain fatty acid beta-oxidation in human tissues, given the reported redundancy?
- question: >-
    Do the STRN3 and DYNLT1 interactions reported in high-throughput screens have any
    physiological relevance to ACOX2 peroxisomal function or regulation?
suggested_experiments:
- description: >-
    Quantitative enzyme kinetics of purified human ACOX2 on THCA-CoA, DHCA-CoA,
    (2S)-pristanoyl-CoA, and straight-chain acyl-CoAs (C10, C16) to define physiological
    substrate preference and confirm the low-efficiency straight-chain activity.
- description: >-
    Tissue-specific metabolic profiling (bile-acid intermediates, branched-chain fatty acids)
    in ACOX2-knockout vs ACOX3-knockout models to disentangle the overlapping branched-chain
    fatty acid roles.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:2079609
  title: Separate peroxisomal oxidases for fatty acyl-CoAs and trihydroxycoprostanoyl-CoA
    in human liver.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Establishes a distinct peroxisomal trihydroxycoprostanoyl-CoA oxidase in human liver
      (i.e. ACOX2), separate from palmitoyl-CoA oxidase; supports peroxisomal localization and
      the bile-acid-intermediate role. Cited quotes verified verbatim against the cached
      abstract.
- id: PMID:27884763
  title: 'ACOX2 deficiency: An inborn error of bile acid synthesis identified in an
    adolescent with persistent hypertransaminasemia.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary experimental (IDA/IMP) source: patient R225W mutation causes accumulation of C27
      intermediates and loss of C24 bile acids; WT (not mutant) ACOX2 enhances THCA to cholic
      acid conversion; peroxisomal localization confirmed by immunofluorescence. Directly
      supports the bile-acid biosynthesis and THCA-CoA oxidase core functions.
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease
    networks.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput (BioPlex) interactome study yielding a bare "protein binding"
      (ACOX2-STRN3) annotation. Correctly cited but functionally uninformative for ACOX2;
      marked as over-annotation.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      HuRI binary (Y2H) interactome map yielding a bare "protein binding" (ACOX2-DYNLT1)
      annotation. Correctly cited but functionally uninformative for ACOX2; marked as
      over-annotation.
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Proteome-scale (BioPlex 3.0) interactome study yielding a bare "protein binding"
      (ACOX2-STRN3) annotation. Correctly cited but functionally uninformative for ACOX2;
      marked as over-annotation.
- id: PMID:8943006
  title: 'Molecular characterization of the human peroxisomal branched-chain acyl-CoA
    oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence
    for the absence of the protein in Zellweger syndrome.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Original molecular characterization of human ACOX2 (hBRCACox): 681-aa protein, C-terminal
      SKL PTS1, peroxisomal (absent in Zellweger livers), human homolog of rat THCC oxidase.
      Supports peroxisomal localization and identity. Quotes verified verbatim.
- id: file:human/ACOX2/ACOX2-uniprot.txt
  title: UniProtKB entry Q99424 (ACOX2_HUMAN), Peroxisomal acyl-coenzyme A oxidase 2
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Curated UniProt record. Source of FUNCTION, catalytic activities (EC 1.3.3.6; Rhea
      reactions for THCA-CoA, pristanoyl-CoA, decanoyl/hexadecanoyl-CoA), FAD cofactor,
      homodimer subunit, peroxisome subcellular location, and CBAS6 disease association.
- id: Reactome:R-HSA-192335
  title: 25(S) THCA-CoA is dehydrogenated to 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA
    (THCA-CoA)
  findings: []
- id: Reactome:R-HSA-193369
  title: 25(S) DHCA-CoA is dehydrogenated to 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
  findings: []
- id: Reactome:R-HSA-389889
  title: ACOX2:FAD, ACOXL:FAD oxidise (2S)-pristanoyl-CoA to trans-2,3-dehydropristanoyl-CoA
  findings: []
- id: Reactome:R-HSA-9033235
  title: Cargo of PEX5S,L translocates from the cytosol to the peroxisomal matrix
  findings: []
- id: Reactome:R-HSA-9033236
  title: PEX5S,L:Cargo binds PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation
    Module)
  findings: []